The problem is as follows: given a directed acyclic graph, where each node is labeled with a character, find all the longest paths of nodes in the graph that form a palindrome.
The initial solution that I thought of was to simply enumerate all the paths in the graph. This effectively generates a bunch of strings, on which we can then apply Manacher's algorithm to find all the longest palindromes. However, this doesn't seem that efficient, since the amount of paths in a graph is exponential in the number of nodes.
Then I started thinking of using dynamic programming directly on the graph, but my problem is that I cannot figure out how to structure my "dynamic programming array". My initial try was to use a 2d boolean array, where array[i][j] == true means that node i to node j is a palindrome but the problem is that there might be multiple paths from i to j.
I've been stuck on this problem for quite a while now I can't seem to figure it out, any help would be appreciated.
The linear-time trick of Manacher's algorithm relies on the fact that if you know that the longest palindrome centered at character 15 has length 5 (chars 13-17), and there's a palindrome centered at node 19 of length 13 (chars 13-25), then you can skip computing the longest palindrome centered at character 23 (23 = 19 + (19 - 15)) because you know it's just going to be the mirror of the one centered at character 15.
With a DAG, you don't have that kind of guarantee because the palindromes can go off in any direction, not just forwards and backwards. However, if you have a candidate palindrome path from node m to node n, whether you can extend that string to a longer palindrome doesn't depend on the path between m and n, but only on m and n (and the graph itself).
Therefore, I'd do this:
First, sort the graph nodes topologically, so that you have an array s[] of node indexes, and there being an edge from s[i] to s[j] implies that i < j.
I'll also assume that you build up an inverse array or hash structure sinv[] such that s[sinv[j]] == j and sinv[s[n]] == n for all integers j in 0..nodeCount-1 and all node indexes n.
Also, I'll assume that you have functions graphPredecessors, graphSuccessors, and graphLetter that take a node index and return the list of predecessors on the graph, the list of successors, or the letter at that node, respectively.
Then, make a two-dimensional array of integers of size nodeCount by nodeCount called r. When r[i][j] = y, and y > 0, it will mean that if there is a palindrome path from a successor of s[i] to a predecessor of s[j], then that path can be extended by adding s[i] to the front and s[j] to the back, and that the extension can be continued by y more nodes (including s[i] and s[j]) in each direction:
for (i=0; i < nodeCount; i++) {
for (j=i; j < nodeCount; j++) {
if (graphLetter(s[i]) == graphLetter(s[j])) {
r[i][j] = 1;
for (pred in graphPredecessors(s[i])) {
for (succ in graphSuccessors(s[j])) {
/* note that by our sorting, sinv[pred] < i <= j < sinv[succ] */
if (r[sinv[pred]][sinv[succ]] >= r[i][j]) {
r[i][j] = 1 + r[sinv[pred]][sinv[succ]];
}
}
}
} else {
r[i][j] = 0;
}
}
}
Then find the maximum value of r[x][x] for x in 0..nodeSize-1, and of r[lft][rgt] where there is an edge from s[lft] to s[rgt]. Call that maximum value M, and say you found it at location [i][j]. Each such i, j pair will represent the center of a longest palindrome path. As long as M is greater than 1, you then extend each center by finding a pred in graphPredecessors(s[i]) and a succ in graphSuccessors(s[j]) such that r[sinv[pred]][sinv[succ]] == M - 1 (the palindrome is now pred->s[i]->s[j]->succ). You then extend that by finding the appropriate index with an r value of M - 2, etc., stopping when you reach a spot where the value in r is 1.
I think this algorithm overall ends up with a runtime of O(V^2 + E^2), but I'm not entirely certain of that.
Related
Problem: Choose an element from the array to maximize the sum after XOR all elements in the array.
Input for problem statement:
N=3
A=[15,11,8]
Output:
11
Approach:
(15^15)+(15^11)+(15^8)=11
My Code for brute force approach:
def compute(N,A):
ans=0
for i in A:
xor_sum=0
for j in A:
xor_sum+=(i^j)
if xor_sum>ans:
ans=xor_sum
return ans
Above approach giving the correct answer but wanted to optimize the approach to solve it in O(n) time complexity. Please help me to get this.
If you have integers with a fixed (constant) number of c bites then it should be possible because O(c) = O(1). For simplicity reasons I assume unsigned integers and n to be odd. If n is even then we sometimes have to check both paths in the tree (see solution below). You can adapt the algorithm to cover even n and negative numbers.
find max in array with length n O(n)
if max == 0 return 0 (just 0s in array)
find the position p of the most significant bit of max O(c) = O(1)
p = -1
while (max != 0)
p++
max /= 2
so 1 << p gives a mask for the highest set bit
build a tree where the leaves are the numbers and every level stands for a position of a bit, if there is an edge to the left from the root then there is a number that has bit p set and if there is an edge to the right there is a number that has bit p not set, for the next level we have an edge to the left if there is a number with bit p - 1 set and an edge to the right if bit p - 1 is not set and so on, this can be done in O(cn) = O(n)
go through the array and count how many times a bit at position i (i from 0 to p) is set => sum array O(cn) = O(n)
assign the root of the tree to node x
now for each i from p to 0 do the following:
if x has only one edge => x becomes its only child node
else if sum[i] > n / 2 => x becomes its right child node
else x becomes its left child node
in this step we choose the best path through the tree that gives us the most ones when xoring O(cn) = O(n)
xor all the elements in the array with the value of x and sum them up to get the result, actually you could have built the result already in the step before by adding sum[i] * (1 << i) to the result if going left and (n - sum[i]) * (1 << i) if going right O(n)
All the sequential steps are O(n) and therefore overall the algorithm is also O(n).
Basically I'm trying to solve this problem :
Given N unit cube blocks, find the smaller number of piles to make in order to use all the blocks. A pile is either a cube or a pyramid. For example two valid piles are the cube 4 *4 *4=64 using 64 blocks, and the pyramid 1²+2²+3²+4²=30 using 30 blocks.
However, I can't find the right angle to approach it. I feel like it's similar to the knapsack problem, but yet, couldn't find an implementation.
Any help would be much appreciated !
First I will give a recurrence relation which will permit to solve the problem recursively. Given N, let
SQUARE-NUMS
TRIANGLE-NUMS
be the subset of square numbers and triangle numbers in {1,...,N} respectively. Let PERMITTED_SIZES be the union of these. Note that, as 1 occurs in PERMITTED_SIZES, any instance is feasible and yields a nonnegative optimum.
The follwing function in pseudocode will solve the problem in the question recursively.
int MinimumNumberOfPiles(int N)
{
int Result = 1 + min { MinimumNumberOfPiles(N-i) }
where i in PERMITTED_SIZES and i smaller than N;
return Result;
}
The idea is to choose a permitted bin size for the items, remove these items (which makes the problem instance smaller) and solve recursively for the smaller instances. To use dynamic programming in order to circumvent multiple evaluation of the same subproblem, one would use a one-dimensional state space, namely an array A[N] where A[i] is the minimum number of piles needed for i unit blocks. Using this state space, the problem can be solved iteratively as follows.
for (int i = 0; i < N; i++)
{
if i is 0 set A[i] to 0,
if i occurs in PERMITTED_SIZES, set A[i] to 1,
set A[i] to positive infinity otherwise;
}
This initializes the states which are known beforehand and correspond to the base cases in the above recursion. Next, the missing states are filled using the following loop.
for (int i = 0; i <= N; i++)
{
if (A[i] is positive infinity)
{
A[i] = 1 + min { A[i-j] : j is in PERMITTED_SIZES and j is smaller than i }
}
}
The desired optimal value will be found in A[N]. Note that this algorithm only calculates the minimum number of piles, but not the piles themselves; if a suitable partition is needed, it has to be found either by backtracking or by maintaining additional auxiliary data structures.
In total, provided that PERMITTED_SIZES is known, the problem can be solved in O(N^2) steps, as PERMITTED_SIZES contains at most N values.
The problem can be seen as an adaptation of the Rod Cutting Problem where each square or triangle size has value 0 and every other size has value 1, and the objective is to minimize the total value.
In total, an additional computation cost is necessary to generate PERMITTED_SIZES from the input.
More precisely, the corresponding choice of piles, once A is filled, can be generated using backtracking as follows.
int i = N; // i is the total amount still to be distributed
while ( i > 0 )
{
choose j such that
j is in PERMITTED_SIZES and j is smaller than i
and
A[i] = 1 + A[i-j] is minimized
Output "Take a set of size" + j; // or just output j, which is the set size
// the part above can be commented as "let's find out how
// the value in A[i] was generated"
set i = i-j; // decrease amount to distribute
}
Local alignment between X and Y, with at least one column aligning a C
to a W.
Given two sequences X of length n and Y of length m, we
are looking for a highest-scoring local alignment (i.e., an alignment
between a substring X' of X and a substring Y' of Y) that has at least
one column in which a C from X' is aligned to a W from Y' (if such an
alignment exists). As scoring model, we use a substitution matrix s
and linear gap penalties with parameter d.
Write a code in order to solve the problem efficiently. If you use dynamic
programming, it suffices to give the equations for computing the
entries in the dynamic programming matrices, and to specify where
traceback starts and ends.
My Solution:
I've taken 2 sequences namely, "HCEA" and "HWEA" and tried to solve the question.
Here is my code. Have I fulfilled what is asked in the question? If am wrong kindly tell me where I've gone wrong so that I will modify my code.
Also is there any other way to solve the question? If its available can anyone post a pseudo code or algorithm, so that I'll be able to code for it.
public class Q1 {
public static void main(String[] args) {
// Input Protein Sequences
String seq1 = "HCEA";
String seq2 = "HWEA";
// Array to store the score
int[][] T = new int[seq1.length() + 1][seq2.length() + 1];
// initialize seq1
for (int i = 0; i <= seq1.length(); i++) {
T[i][0] = i;
}
// Initialize seq2
for (int i = 0; i <= seq2.length(); i++) {
T[0][i] = i;
}
// Compute the matrix score
for (int i = 1; i <= seq1.length(); i++) {
for (int j = 1; j <= seq2.length(); j++) {
if ((seq1.charAt(i - 1) == seq2.charAt(j - 1))
|| (seq1.charAt(i - 1) == 'C') && (seq2.charAt(j - 1) == 'W')) {
T[i][j] = T[i - 1][j - 1];
} else {
T[i][j] = Math.min(T[i - 1][j], T[i][j - 1]) + 1;
}
}
}
// Strings to store the aligned sequences
StringBuilder alignedSeq1 = new StringBuilder();
StringBuilder alignedSeq2 = new StringBuilder();
// Build for sequences 1 & 2 from the matrix score
for (int i = seq1.length(), j = seq2.length(); i > 0 || j > 0;) {
if (i > 0 && T[i][j] == T[i - 1][j] + 1) {
alignedSeq1.append(seq1.charAt(--i));
alignedSeq2.append("-");
} else if (j > 0 && T[i][j] == T[i][j - 1] + 1) {
alignedSeq2.append(seq2.charAt(--j));
alignedSeq1.append("-");
} else if (i > 0 && j > 0 && T[i][j] == T[i - 1][j - 1]) {
alignedSeq1.append(seq1.charAt(--i));
alignedSeq2.append(seq2.charAt(--j));
}
}
// Display the aligned sequence
System.out.println(alignedSeq1.reverse().toString());
System.out.println(alignedSeq2.reverse().toString());
}
}
#Shole
The following are the two question and answers provided in my solved worksheet.
Aligning a suffix of X to a prefix of Y
Given two sequences X and Y, we are looking for a highest-scoring alignment between any suffix of X and any prefix of Y. As a scoring model, we use a substitution matrix s and linear gap penalties with parameter d.
Give an efficient algorithm to solve this problem optimally in time O(nm), where n is the length of X and m is the length of Y. If you use a dynamic programming approach, it suffices to give the equations that are needed to compute the dynamic programming matrix, to explain what information is stored for the traceback, and to state where the traceback starts and ends.
Solution:
Let X_i be the prefix of X of length i, and let Y_j denote the prefix of Y of length j. We compute a matrix F such that F[i][j] is the best score of an alignment of any suffix of X_i and the string Y_j. We also compute a traceback matrix P. The computation of F and P can be done in O(nm) time using the following equations:
F[0][0]=0
for i = 1..n: F[i][0]=0
for j = 1..m: F[0][j]=-j*d, P[0][j]=L
for i = 1..n, j = 1..m:
F[i][j] = max{ F[i-1][j-1]+s(X[i-1],Y[j-1]), F[i-1][j]-d, F[i][j-1]-d }
P[i][j] = D, T or L according to which of the three expressions above is the maximum
Once we have computed F and P, we find the largest value in the bottom row of the matrix F. Let F[n][j0] be that largest value. We start traceback at F[n][j0] and continue traceback until we hit the first column of the matrix. The alignment constructed in this way is the solution.
Aligning Y to a substring of X, without gaps in Y
Given a string X of length n and a string Y of length m, we want to compute a highest-scoring alignment of Y to any substring of X, with the extra constraint that we are not allowed to insert any gaps into Y. In other words, the output is an alignment of a substring X' of X with the string Y, such that the score of the alignment is the largest possible (among all choices of X') and such that the alignment does not introduce any gaps into Y (but may introduce gaps into X'). As a scoring model, we use again a substitution matrix s and linear gap penalties with parameter d.
Give an efficient dynamic programming algorithm that solves this problem optimally in polynomial time. It suffices to give the equations that are needed to compute the dynamic programming matrix, to explain what information is stored for the traceback, and to state where the traceback starts and ends. What is the running-time of your algorithm?
Solution:
Let X_i be the prefix of X of length i, and let Y_j denote the prefix of Y of length j. We compute a matrix F such that F[i][j] is the best score of an alignment of any suffix of X_i and the string Y_j, such that the alignment does not insert gaps in Y. We also compute a traceback matrix P. The computation of F and P can be done in O(nm) time using the following equations:
F[0][0]=0
for i = 1..n: F[i][0]=0
for j = 1..m: F[0][j]=-j*d, P[0][j]=L
for i = 1..n, j = 1..m:
F[i][j] = max{ F[i-1][j-1]+s(X[i-1],Y[j-1]), F[i][j-1]-d }
P[i][j] = D or L according to which of the two expressions above is the maximum
Once we have computed F and P, we find the largest value in the rightmost column of the matrix F. Let F[i0][m] be that largest value. We start traceback at F[i0][m] and continue traceback until we hit the first column of the matrix. The alignment constructed in this way is the solution.
Hope you get some idea about wot i really need.
I think it's quite easy to find resources or even the answer by google...as the first result of the searching is already a thorough DP solution.
However, I appreciate that you would like to think over the solution by yourself and are requesting some hints.
Before I give out some of the hints, I would like to say something about designing a DP solution
(I assume you know this can be solved by a DP solution)
A dp solution basically consisting of four parts:
1. DP state, you have to self define the physical meaning of one state, eg:
a[i] := the money the i-th person have;
a[i][j] := the number of TV programmes between time i and time j; etc
2. Transition equations
3. Initial state / base case
4. how to query the answer, eg: is the answer a[n]? or is the answer max(a[i])?
Just some 2 cents on a DP solution, let's go back to the question :)
Here's are some hints I am able to think of:
What is the dp state? How many dimensions are enough to define such a state?
Thinking of you are solving problems much alike to common substring problem (on 2 strings),
1-dimension seems too little and 3-dimensions seems too many right?
As mentioned in point 1, this problem is very similar to common substring problem, maybe you should have a look on these problems to get yourself some idea?
LCS, LIS, Edit Distance, etc.
Supplement part: not directly related to the OP
DP is easy to learn, but hard to master. I know a very little about it, really cannot share much. I think "Introduction to algorithm" is a quite standard book to start with, you can find many resources, especially some ppt/ pdf tutorials of some colleges / universities to learn some basic examples of DP.(Learn these examples is useful and I'll explain below)
A problem can be solved by many different DP solutions, some of them are much better (less time / space complexity) due to a well-defined DP state.
So how to design a better DP state or even get the sense that one problem can be solved by DP? I would say it's a matter of experiences and knowledge. There are a set of "well-known" DP problems which I would say many other DP problems can be solved by modifying a bit of them. Here is a post I just got accepted about another DP problem, as stated in that post, that problem is very similar to a "well-known" problem named "matrix chain multiplication". So, you cannot do much about the "experience" part as it has no express way, yet you can work on the "knowledge" part by studying these standard DP problems first maybe?
Lastly, let's go back to your original question to illustrate my point of view:
As I knew LCS problem before, I have a sense that for similar problem, I may be able to solve it by designing similar DP state and transition equation? The state s(i,j):= The optimal cost for A(1..i) and B(1..j), given two strings A & B
What is "optimal" depends on the question, and how to achieve this "optimal" value in each state is done by the transition equation.
With this state defined, it's easy to see the final answer I would like to query is simply s(len(A), len(B)).
Base case? s(0,0) = 0 ! We can't really do much on two empty string right?
So with the knowledge I got, I have a rough thought on the 4 main components of designing a DP solution. I know it's a bit long but I hope it helps, cheers.
I've a set of string [S1 S2 S3 ... Sn] and I'm to count all such target strings T such that each one of S1 S2... Sn can be converted into T within a total of K edits. All the strings are of fixed length L and an edit here is hamming distance.
All I've is sort of brute force approach.
so, If my alphabet size is 4, I've sample space of O(4^L) and it takes O(L) time to check each one of them. I can't seem to bring down the complexity from exponential to some poly or pseudo-poly! Is there any way to prune down the sample space to do better?
I tried to visualize it as in a L-dimensional vector space. I've been given N points and have to count all the points whose sum of distance from the given N points is less than or equal to K. i.e. d1 + d2 + d3 +...+ dN <= K
Is there any known geometric algorithm which solves this or similar problem with a better complexity? Kindly point me in the right direction or any hints are appreciated.
Thank you
You can do this efficiently with dynamic programming.
The key idea is that you don't need to enumerate all possible target strings, you just need to know how many ways targets are possible with K edits considering only the string indicies after I.
alphabet = 'abcd'
s = [ 'aabbbb', 'bacaaa', 'dabbbb', 'cabaaa']
# use memoized from http://wiki.python.org/moin/PythonDecoratorLibrary
#memoized
def count(edits_left, index):
if index == -1 and edits_left >= 0:
return 1
if edits_left < 0:
return 0
ret = 0
for char in alphabet:
edits_used = 0
for mutate_str in s:
if mutate_str[index] != char:
edits_used += 1
ret += count(edits_left - edits_used, index - 1)
return ret
Thinking out loud, it seems to me that this problem boils down to a combinatorial problem.
In general for a string S of length L, there are a total of C(L,K) (binomial coefficient) positions that can be substituted and therefore (ALPHABET_SIZE^K)*C(L,K) target strings T from a Hamming Distance of K.
Binomial Coefficient can be computed quite easily using Dynamic Programming and the Pascal Triangle... No need to get crazy into factoriel etc...
Now that one string case is treated, dealing with multiple strings is a little bit more tricky since you might double count targets. Intuitively though if S1 is K far from S2 then both string will generate the same set of target so you don't double count in this case. This last statement might be a long shot that's why I made sure to say "intuitively" :)
Hope it helps,
This is not a homework problem. I am reviewing myself of the Longest Increasing Subsequence problem. I read every where online. I understand how to find the "length", but I don't understand how to back-trace the actual sequence. I am using the patience sorting algorithm to find the length. Can anyone explain how to find the actual sequence? I do not really understand the version in Wikipedia. Can someone explain in a different method or different way?
Thanks.
Lets define as max(j) as the longest increasing subsequence up to A[j]. There are two options: or we use A[j] in this subsequence, or we don't.
If we dont use it, then the value will be max(j-1). If we do use it, then the value will be
max(i)+1, when i is the biggest index such that i < j and A[i] < A[j]. (Here we assume that the max(i) sequence uses i- not neccessary true, but we can solve this issue by saving for each cell 2 values- the max(j) value, and max*(j), when max*(j) is the longest increasing subsequence up to A[j] that uses A[j]. max*(j) will be calculated each time as max*(i)+1).
To sum up, the recursive formula for calculating max(j) will be:
max{max(j-1),max*(i)+1},and max*(j)= max*(i)+1.
In each array cell you can save a pointer, that tells you if you chose to use the A[j] cell or not. In this way you can find all the sequence while moving backwards on the array.
Time Complexity: The complexity of the recursive formula and finding the sequence at the end is O(n). The problem here is finding for each A[j] the corresponding A[i] such that i is the biggest index such that i < j, A[i] < A[j].
Of course you can do it naivly in O(n^2) (from each cell go backwards until you find this i). If you want to do better then I'm pretty sure that you can do it in O(nlogn) in the following way:
*Sort your Array.
1) go for the smallest integer in the array, and notate is position in the array as k.
2)For A[k+1], we have of course A[k] < A[k+1]. If A[k+1]>A[k+2] then k will feet to the k+2 cell as well, and so on until we have A[k+m] < A[k+m+1], and then k+m is feet to k+m+1,
3)delete all the cells that you found thier corresponding cell in the previous stage
4) return to 1.
Hoped that it help. Please notice that I thought about it all alone, therefore there is a very small chance that there is some mistake here- please be convinced that I'm right and ask for more clarifications, if you need.
This Python code solves the Longest Increasing Sequence problem, and also returns one of such sequences. The trick is, at the same time that the dynamic programming table gets filled, another array is also filled, storing the index of the elements that were used to construct the optimal solution.
def an_lis(nums):
table, solution = lis_table(nums)
if not table:
return (0, [])
n, maxLen = max(enumerate(table), key=itemgetter(1))
lis = [nums[n]]
while solution[n] != -1:
lis.append(nums[solution[n]])
n = solution[n]
return lis[::-1]
def lis_table(nums):
n = len(nums)
table, solution = [0] * n, [-1] * n
for i in xrange(n):
maxLen, maxIdx = 0, -1
for j in xrange(i):
if nums[j] < nums[i] and table[j] > maxLen:
maxLen, maxIdx = table[j], j
table[i], solution[i] = 1 + maxLen, maxIdx
return (table, solution)